public function getPolicy()
{
$att = Attribute::model()->findByAttributes(array('attribute_name' => Attribute::FUP));
if (!$att) {
return null;
}
return DatasetAttributes::model()->findByAttributes(array('dataset_id' => $this->id, 'attribute_id' => $att->id));
}
public function actionCreate()
{
$model = new DatasetAttributes();
$att = Attribute::model()->findByAttributes(array('attribute_name' => Attribute::FUP));
if (!$att) {
$att = new Attribute();
$att->attribute_name = Attribute::FUP;
$att->definition = '';
$att->save();
}
$model->attribute_id = $att->id;
$image = new Images();
if (isset($_POST['DatasetAttributes'])) {
$args = $_POST['DatasetAttributes'];
$exist = DatasetAttributes::model()->findByAttributes(array('dataset_id' => $args['dataset_id'], 'attribute_id' => $att->id));
if ($exist) {
$model = $exist;
}
$model->attributes = $args;
$model->value = '';
//$image->attributes = $_POST['Images'];
$image->license = "no license";
$image->photographer = "no author";
$image->source = "gigadb";
if ($image->validate()) {
$image->save();
} else {
Yii::log(print_r($image->getErrors(), true), 'debug');
}
if ($image) {
$model->image_id = $image->id;
}
if ($model->validate()) {
$model->save();
$this->redirect('/dataset/' . $model->dataset->identifier);
} else {
Yii::log(print_r($model->getErrors(), true), 'debug');
}
}
$this->render('create', array('model' => $model, 'image' => $image));
}
public function actionPxInfoManagement()
{
if (!isset($_GET['id'])) {
$this->redirect("/user/view_profile");
} else {
$dataset = Dataset::model()->findByPk($_GET['id']);
if (!$dataset) {
Yii::log('dataset id not found', 'debug');
$this->redirect("/user/view_profile");
}
if ($dataset->submitter_id != Yii::app()->user->id) {
Yii::log('not the owner', 'debug');
Yii::app()->user->setFlash('keyword', "You are not the owner of dataset");
$this->redirect("/user/view_profile");
}
# load attributes
$keywordsAttr = Attribute::model()->findByAttributes(array('attribute_name' => 'PX_keywords'));
$sppAttr = Attribute::model()->findByAttributes(array('attribute_name' => 'PX_sample_processing_protocol'));
$dppAttr = Attribute::model()->findByAttributes(array('attribute_name' => 'PX_data_processing_protocol'));
$expTypeAttr = Attribute::model()->findByAttributes(array('attribute_name' => 'PX_experiment_type'));
$instrumentAttr = Attribute::model()->findByAttributes(array('attribute_name' => 'PX_instrument'));
$quantificationAttr = Attribute::model()->findByAttributes(array('attribute_name' => 'PX_quantification'));
$modificationAttr = Attribute::model()->findByAttributes(array('attribute_name' => 'PX_modification'));
if (!$keywordsAttr or !$sppAttr or !$dppAttr or !$expTypeAttr or !$instrumentAttr or !$quantificationAttr or !$modificationAttr) {
Yii::app()->user->setFlash('keyword', "Attr cannot be found.");
Yii::log("Attr cannot be found.", 'debug');
$this->redirect("/user/view_profile");
}
# create new pxForm for validation and store px info into pxForm
$pxForm = new PxInfoForm();
# load keywords
$keywords = DatasetAttributes::model()->findByAttributes(array('dataset_id' => $dataset->id, 'attribute_id' => $keywordsAttr->id));
if (!$keywords) {
$keywords = new DatasetAttributes();
$keywords->dataset_id = $dataset->id;
$keywords->attribute_id = $keywordsAttr->id;
}
$pxForm->keywords = $keywords->value;
# load sample processing protocol
$criteria = new CDbCriteria();
$criteria->join = 'LEFT JOIN sample s on (t.sample_id = s.id) LEFT JOIN dataset_sample ds on (ds.sample_id = s.id)';
$criteria->addCondition('ds.dataset_id = ' . $dataset->id);
$criteria->addCondition('t.attribute_id = ' . $sppAttr->id);
$spp = SampleAttribute::model()->find($criteria);
if ($spp) {
# get one spp
$pxForm->spp = $spp->value;
}
# load experiment first, if not create one
$experiment = Experiment::model()->findByAttributes(array('dataset_id' => $dataset->id));
if (!$experiment) {
#create new experiment
$experiment = new Experiment();
$experiment->experiment_type = 'proteomic';
$experiment->experiment_name = 'PX "' . $dataset->title . '"';
$experiment->dataset_id = $dataset->id;
$experiment->save(false);
}
# load data processing protocol
$dpp = ExpAttributes::model()->findByAttributes(array('exp_id' => $experiment->id, 'attribute_id' => $dppAttr->id));
if (!$dpp) {
$dpp = new ExpAttributes();
$dpp->exp_id = $experiment->id;
$dpp->attribute_id = $dppAttr->id;
}
$pxForm->dpp = $dpp->value;
# load experiment type
$expType = ExpAttributes::model()->findByAttributes(array('exp_id' => $experiment->id, 'attribute_id' => $expTypeAttr->id));
if (!$expType) {
# set default experiment type
$expType = new ExpAttributes();
$expType->exp_id = $experiment->id;
$expType->attribute_id = $expTypeAttr->id;
$expType->value = CJSON::encode(array());
}
$expTypeVal = CJSON::decode($expType->value);
$pxForm->experimentType = $expTypeVal;
if (isset($expTypeVal['Other'])) {
$pxForm->exTypeOther = $expTypeVal['Other'];
}
# load instrument
$instrument = ExpAttributes::model()->findByAttributes(array('exp_id' => $experiment->id, 'attribute_id' => $instrumentAttr->id));
if (!$instrument) {
# set default instrument
$instrument = new ExpAttributes();
$instrument->exp_id = $experiment->id;
$instrument->attribute_id = $instrumentAttr->id;
$instrument->value = CJSON::encode(array());
}
$insVal = CJSON::decode($instrument->value);
$pxForm->instrument = $insVal;
if (isset($insVal['Other'])) {
$pxForm->instrumentOther = $insVal['Other'];
}
# load quantification
$quantification = ExpAttributes::model()->findByAttributes(array('exp_id' => $experiment->id, 'attribute_id' => $quantificationAttr->id));
if (!$quantification) {
# set default quantification
$quantification = new ExpAttributes();
$quantification->exp_id = $experiment->id;
$quantification->attribute_id = $quantificationAttr->id;
$quantification->value = CJSON::encode(array());
}
$quanVal = CJSON::decode($quantification->value);
$pxForm->quantification = $quanVal;
if (isset($quanVal['Other'])) {
$pxForm->quantificationOther = $quanVal['Other'];
}
# load modification
$modification = ExpAttributes::model()->findByAttributes(array('exp_id' => $experiment->id, 'attribute_id' => $modificationAttr->id));
if (!$modification) {
# set default modificaiton
$modification = new ExpAttributes();
$modification->exp_id = $experiment->id;
$modification->attribute_id = $modificationAttr->id;
$modification->value = CJSON::encode(array());
}
$modiVal = CJSON::decode($modification->value);
$pxForm->modification = $modiVal;
if (isset($modiVal['Other'])) {
$pxForm->modificationOther = $modiVal['Other'];
}
if (isset($_POST['PxInfoForm'])) {
# default is save and quit, redirect to user view_profile page
$isSubmit = false;
if (isset($_POST['submit-btn'])) {
# if user click submit, then submit the dataset
$isSubmit = true;
}
# store px Info
$transaction = Yii::app()->db->beginTransaction();
try {
$attrs = $_POST['PxInfoForm'];
$pxForm->attributes = $attrs;
if ($pxForm->validate()) {
#store keywords
$keywords->value = $attrs['keywords'];
#store dpp
$dpp->value = $attrs['dpp'];
if (isset($_POST['exType'])) {
#store exp type
$expTypeVal = $_POST['exType'];
if (isset($expTypeVal['Other'])) {
$expTypeVal['Other'] = $attrs['exTypeOther'] ? $attrs['exTypeOther'] : "";
}
$expType->value = CJSON::encode($expTypeVal);
}
if (isset($_POST['quantification'])) {
#store quantification
$quanVal = $_POST['quantification'];
if (isset($quanVal['Other'])) {
$quanVal['Other'] = $attrs['quantificationOther'] ? $attrs['quantificationOther'] : "";
}
$quantification->value = CJSON::encode($quanVal);
}
if (isset($_POST['instrument'])) {
#store instrument
$insVal = $_POST['instrument'];
if (isset($insVal['Other'])) {
$insVal['Other'] = $attrs['instrumentOther'] ? $attrs['instrumentOther'] : "";
}
$instrument->value = CJSON::encode($insVal);
}
if (isset($_POST['modification'])) {
#store modification
$modiVal = $_POST['modification'];
if (isset($modiVal['Other'])) {
$modiVal['Other'] = $attrs['modificationOther'] ? $attrs['modificationOther'] : "";
}
$modification->value = CJSON::encode($modiVal);
}
#store spp into each samples in the dataset
$samples = $dataset->allSamples;
$isSppsStored = $this->storeSpps($samples, $attrs['spp'], $sppAttr);
if ($isSppsStored and $keywords->save() and $dpp->save() and $expType->save() and $quantification->save() and $instrument->save() and $modification->save()) {
$transaction->commit();
if ($isSubmit) {
$this->redirect(array('/dataset/submit', 'id' => $dataset->id));
}
$this->redirect('/user/view_profile');
}
}
} catch (Exception $e) {
$message = $e->getMessage();
Yii::log(print_r($message, true), 'error');
$transaction->rollback();
$this->redirect('/');
}
}
$this->render('pxInfoManagement', array('model' => $dataset, 'pxForm' => $pxForm));
}
}
